HBO1 catalyzes lysine lactylation and mediates histone H3K9la to regulate gene transcription

Lysine lactylation (Kla) links metabolism and gene regulation and plays a key role in multiple biological processes. However, the regulatory mechanism and functional consequence of Kla remain to be explored. Here, we report that HBO1 functions as a lysine lactyltransferase to regulate transcription. We show that HBO1 catalyzes the addition of Kla in vitro and intracellularly, and E508 is a key site for the lactyltransferase activity of HBO1. Quantitative proteomic analysis further reveals 95 endogenous Kla sites targeted by HBO1, with the majority located on histones. Using site-specific antibodies, we find that HBO1 may preferentially catalyze histone H3K9la and scaffold proteins including JADE1 and BRPF2 can promote the enzymatic activity for histone Kla. Notably, CUT&Tag assays demonstrate that HBO1 is required for histone H3K9la on transcription start sites (TSSs). Besides, the regulated Kla can promote key signaling pathways and tumorigenesis, which is further supported by evaluating the malignant behaviors of HBO1- knockout (KO) tumor cells, as well as the level of histone H3K9la in clinical tissues. Our study reveals HBO1 serves as a lactyltransferase to mediate a histone Kla-dependent gene transcription.


Reporting on sex and gender
Reporting on race, ethnicity, or other socially relevant groupings

Recruitment
Ethics oversight Note that full information on the approval of the study protocol must also be provided in the manuscript.

Field-specific reporting
Please select the one below that is the best fit for your research.If you are not sure, read the appropriate sections before making your selection.

Life sciences
Behavioural & social sciences Ecological, evolutionary & environmental sciences For a reference copy of the document with all sections, see nature.com/documents/nr-reporting-summary-flat.pdf

Life sciences study design
All studies must disclose on these points even when the disclosure is negative.The raw data generated in this study are provided in the Source Data file.All data needed to evaluate the conclusions in the paper are present in the paper, the Supplementary information and Source Data file.
All the patients of commercial tissue microarray containing 84 cervial cancer and 52 para-tumor tissues are female.
All the patients of commercial tissue microarray containing 84 cervial cancer and 52 para-tumor tissues are Chinese.
Information not collected.A commercial tissue microarray containing 84 cervial cancer and 52 para-tumor tissues were purchased from Shanghai Zhuoli Biotech company.
We did not recruit any patients in this study.A commercial tissue microarray containing 84 cervial cancer and 52 para-tumor tissues were purchased from Shanghai Zhuoli Biotech company.
Cervical tumor tissue microarray ZL-Utrsur1601 was purchased from WELLBI.Our study complies with all relevant ethical regulations and was approved by the Ethics Committee of Shanghai Zhuoli Biotech Company (Shanghai, China) (Ethics number: ZLL-15-01).
Samples of 84 cervical cancer cells and 52 normal cervical samples were used.The cell samples were not predetermined, we used HeLa cells, HEK293T cells, HepG2 cells, U87MG cells, MDA-MB-231 cells, KYSE-30 cells, HCT116 cells and H460 cells as study samples, and all the experiments were biologically repeated at least three times.
No data were excluded.
All experiments were successfully replicated at least three independent biological experiments, except SILAC MS was performed once and CUT&Tag was performed twice.In the SILAC MS experiment, we strictly controlled the labeling efficiency of isotopes above 98%.In the process of SILAC experiment, heavy and light samples are mixed, digested and identified at the same time, which greatly reduces the errors caused by equipment and experimental operation, thus the results of SILAC experiment have relatively high accuracy.At the same time, we also conducted biological verification of the accuracy of SILAC MS results.Chip-qPCR was performed to guarantee the accuracy of differential gene between WT and HBO1-KO .
No randomization was necessary as only single variables changed per experiment.Sex and/or gender were not taken into account in this study.
Not applicable.Any phenotypic assessment or other measurements was performed using discrete, quantitative measurements.

nature portfolio | reporting summary
April 2023 Reporting for specific materials, systems and methods The mass spectrometry proteomics data have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifier PXD051415 [http://www.ebi.ac.uk/pride/archive/projects/PXD051415].The CUT&Tag data generated in this study have been deposited in the Gene Expression Omnibus (GEO) repository under accession code GSE239656 [https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE239656].
We require information from authors about some types of materials, experimental systems and methods used in many studies.Here, indicate whether each material, system or method listed is relevant to your study.If you are not sure if a list item applies to your research, read the appropriate section before selecting a response.